error
Closed this issue · 7 comments
作者您好，我在运行predict_single.py 是遇到了一些索引上的错误，不知道如何去解决它。希望作者能给我提供一些帮助
Original Traceback (most recent call last):
File "/nas2_public/soft/Miniforge-pypy3-23.11.0-0/envs/ConBAP_01/lib/python3.9/site-packages/torch/utils/data/_utils/worker.py", line 302, in _worker_loop
data = fetcher.fetch(index)
File "/nas2_public/soft/Miniforge-pypy3-23.11.0-0/envs/ConBAP_01/lib/python3.9/site-packages/torch/utils/data/_utils/fetch.py", line 52, in fetch
return self.collate_fn(data)
File "/nas2_public/yangjie_data/New/2.ConBAP/ConBAP-main/supervised/dataset_ConBAP.py", line 272, in collate_fn
graphA = batchA[i]
File "/nas2_public/soft/Miniforge-pypy3-23.11.0-0/envs/ConBAP_01/lib/python3.9/site-packages/torch_geometric/data/batch.py", line 148, in getitem
return self.get_example(idx)
File "/nas2_public/soft/Miniforge-pypy3-23.11.0-0/envs/ConBAP_01/lib/python3.9/site-packages/torch_geometric/data/batch.py", line 96, in get_example
data = separate(
File "/nas2_public/soft/Miniforge-pypy3-23.11.0-0/envs/ConBAP_01/lib/python3.9/site-packages/torch_geometric/data/separate.py", line 38, in separate
data_store[attr] = _separate(attr, batch_store[attr], idx, slices,
File "/nas2_public/soft/Miniforge-pypy3-23.11.0-0/envs/ConBAP_01/lib/python3.9/site-packages/torch_geometric/data/separate.py", line 64, in _separate
start, end = int(slices[idx]), int(slices[idx + 1])
IndexError: index 2 is out of bounds for dimension 0 with size 2
Hello! Can you provide your input as well? It can help with debug
Hello, is the second column of your .CSV file set correctly? If you are using it to predict your own data set, please use predict.py. The affinities in the second column need to be all set to 0. As mentioned above, can you provide your input files?
Thank you for your reply. I use the raw data you provided on github. The same error still occurs after I set the affinity of the toy_set.csv file to 0. In addition, I use the proteins and ligands provided by CASF2016 (more than 20 complexes such as 1a30 and 1h22) and get the same error.
Can you provide all the package version in your conda environment?
anyio==4.3.0
argon2-cffi==23.1.0
argon2-cffi-bindings==21.2.0
arrow==1.3.0
asttokens @ file:///opt/conda/conda-bld/asttokens_1646925590279/work
async-lru==2.0.4
attrs==23.2.0
Babel==2.14.0
backcall @ file:///home/ktietz/src/ci/backcall_1611930011877/work
beautifulsoup4==4.12.3
biopython==1.83
bleach==6.1.0
Bottleneck @ file:///croot/bottleneck_1707864210935/work
Brotli @ file:///home/conda/feedstock_root/build_artifacts/brotli-split_1695989787169/work
certifi @ file:///home/conda/feedstock_root/build_artifacts/certifi_1707022139797/work/certifi
cffi==1.16.0
charset-normalizer @ file:///home/conda/feedstock_root/build_artifacts/charset-normalizer_1698833585322/work
colorama @ file:///croot/colorama_1672386526460/work
comm @ file:///croot/comm_1709322850197/work
contourpy @ file:///croot/contourpy_1700583582875/work
cycler @ file:///tmp/build/80754af9/cycler_1637851556182/work
debugpy @ file:///croot/debugpy_1690905042057/work
decorator @ file:///opt/conda/conda-bld/decorator_1643638310831/work
defusedxml==0.7.1
exceptiongroup @ file:///croot/exceptiongroup_1706031385326/work
executing @ file:///opt/conda/conda-bld/executing_1646925071911/work
fastjsonschema==2.19.1
fonttools==4.25.0
fqdn==1.5.1
googledrivedownloader==0.4
h11==0.14.0
httpcore==1.0.5
httpx==0.27.0
idna @ file:///home/conda/feedstock_root/build_artifacts/idna_1701026962277/work
importlib-metadata @ file:///croot/importlib_metadata-suite_1704813515092/work
importlib-resources @ file:///croot/importlib_resources-suite_1704281845041/work
ipykernel @ file:///croot/ipykernel_1705933831282/work
ipython @ file:///croot/ipython_1694181358621/work
ipywidgets==8.1.2
isodate==0.6.1
isoduration==20.11.0
jedi @ file:///tmp/build/80754af9/jedi_1644297102865/work
Jinja2==3.1.3
joblib @ file:///croot/joblib_1685113087166/work
json5==0.9.24
jsonpointer==2.4
jsonschema==4.21.1
jsonschema-specifications==2023.12.1
jupyter==1.0.0
jupyter-console==6.6.3
jupyter-events==0.10.0
jupyter-lsp==2.2.4
jupyter_client @ file:///croot/jupyter_client_1699455897726/work
jupyter_core @ file:///croot/jupyter_core_1698937308754/work
jupyter_server==2.13.0
jupyter_server_terminals==0.5.3
jupyterlab==4.1.5
jupyterlab_pygments==0.3.0
jupyterlab_server==2.25.4
jupyterlab_widgets==3.0.10
kiwisolver @ file:///croot/kiwisolver_1672387140495/work
MarkupSafe==2.1.5
matplotlib @ file:///croot/matplotlib-suite_1693812469450/work
matplotlib-inline @ file:///opt/conda/conda-bld/matplotlib-inline_1662014470464/work
mistune==3.0.2
mkl-fft @ file:///croot/mkl_fft_1695058164594/work
mkl-random @ file:///croot/mkl_random_1695059800811/work
mkl-service==2.4.0
munkres==1.1.4
nbclient==0.10.0
nbconvert==7.16.3
nbformat==5.10.3
nest-asyncio @ file:///croot/nest-asyncio_1708532673751/work
networkx @ file:///croot/networkx_1690561992265/work
notebook==7.1.2
notebook_shim==0.2.4
numexpr @ file:///croot/numexpr_1696515281613/work
numpy @ file:///work/mkl/numpy_and_numpy_base_1682953417311/work
overrides==7.7.0
packaging @ file:///croot/packaging_1710807400464/work
pandas==1.4.4
pandocfilters==1.5.1
parso @ file:///opt/conda/conda-bld/parso_1641458642106/work
pexpect @ file:///tmp/build/80754af9/pexpect_1605563209008/work
pickleshare @ file:///tmp/build/80754af9/pickleshare_1606932040724/work
pillow @ file:///croot/pillow_1707233021655/work
platformdirs @ file:///croot/platformdirs_1692205439124/work
ply==3.11
Pmw @ file:///home/conda/feedstock_root/build_artifacts/pmw_1695847164449/work
prometheus_client==0.20.0
prompt-toolkit @ file:///croot/prompt-toolkit_1704404351921/work
psutil @ file:///opt/conda/conda-bld/psutil_1656431268089/work
ptyprocess @ file:///tmp/build/80754af9/ptyprocess_1609355006118/work/dist/ptyprocess-0.7.0-py2.py3-none-any.whl
pure-eval @ file:///opt/conda/conda-bld/pure_eval_1646925070566/work
pycparser==2.22
Pygments @ file:///croot/pygments_1684279966437/work
pymol==2.5.0
pyparsing @ file:///opt/conda/conda-bld/pyparsing_1661452539315/work
PyQt5==5.15.10
PyQt5-sip @ file:///croot/pyqt-split_1698769088074/work/pyqt_sip
PySocks @ file:///home/conda/feedstock_root/build_artifacts/pysocks_1661604839144/work
python-dateutil @ file:///tmp/build/80754af9/python-dateutil_1626374649649/work
python-json-logger==2.0.7
pytz @ file:///croot/pytz_1695131579487/work
PyYAML==6.0.1
pyzmq @ file:///croot/pyzmq_1705605076900/work
qtconsole==5.5.1
QtPy==2.4.1
rdflib==7.0.0
rdkit==2022.9.5
referencing==0.34.0
requests @ file:///home/conda/feedstock_root/build_artifacts/requests_1684774241324/work
rfc3339-validator==0.1.4
rfc3986-validator==0.1.1
rpds-py==0.18.0
scikit-learn @ file:///croot/scikit-learn_1694788527225/work
scipy @ file:///home/conda/feedstock_root/build_artifacts/scipy_1604204601456/work
seaborn @ file:///croot/seaborn_1673479180098/work
Send2Trash==1.8.2
sip @ file:///croot/sip_1698675935381/work
six @ file:///tmp/build/80754af9/six_1644875935023/work
sniffio==1.3.1
soupsieve==2.5
stack-data @ file:///opt/conda/conda-bld/stack_data_1646927590127/work
terminado==0.18.1
threadpoolctl @ file:///Users/ktietz/demo/mc3/conda-bld/threadpoolctl_1629802263681/work
tinycss2==1.2.1
tomli @ file:///opt/conda/conda-bld/tomli_1657175507142/work
torch==1.12.1
torch-cluster @ file:///home/rxdcpu/torch-1.12.1%2Bcu116/torch_cluster-1.6.0%2Bpt112cu116-cp39-cp39-linux_x86_64.whl#sha256=6a01cd6b7452d8029d41812fb1683ee483e6a68e82490ab8681c73d90db8b2a5
torch-scatter @ file:///home/rxdcpu/torch-1.12.1%2Bcu116/torch_scatter-2.1.0%2Bpt112cu116-cp39-cp39-linux_x86_64.whl#sha256=b8d8f271e848655061de2d21a4d4903f8a0a7824e57acf3e2b4e52694758fcff
torch-sparse @ file:///home/rxdcpu/torch-1.12.1%2Bcu116/torch_sparse-0.6.16%2Bpt112cu116-cp39-cp39-linux_x86_64.whl#sha256=8661a72231ee0d008a79f9b528786500ed76f7020d63347a0ea6ab3079937b79
torch-spline-conv @ file:///home/rxdcpu/torch-1.12.1%2Bcu116/torch_spline_conv-1.2.1%2Bpt112cu116-cp39-cp39-linux_x86_64.whl#sha256=9d7e2d4734e8d3115c2db6f4e2e31ad23d20c228c87421ab3d05353e8ebd5cda
torch_geometric==2.0.3
torchaudio==0.12.1
torchvision==0.13.1
tornado @ file:///croot/tornado_1696936946304/work
tqdm @ file:///opt/conda/conda-bld/tqdm_1647339053476/work
traitlets @ file:///croot/traitlets_1671143879854/work
types-python-dateutil==2.9.0.20240316
typing_extensions @ file:///home/conda/feedstock_root/build_artifacts/typing_extensions_1708904622550/work
tzdata @ file:///croot/python-tzdata_1690578112552/work
uri-template==1.3.0
urllib3 @ file:///home/conda/feedstock_root/build_artifacts/urllib3_1708239446578/work
wcwidth @ file:///Users/ktietz/demo/mc3/conda-bld/wcwidth_1629357192024/work
webcolors==1.13
webencodings==0.5.1
websocket-client==1.7.0
widgetsnbextension==4.0.10
yacs==0.1.8
I found a bug，please install pyg==2.3.0 and try it again
Thank you very much for your help! I have solved this problem, and I'm sorry for taking your time to help me. If given the opportunity, I look forward to further academic exchanges with you.